Some of Kronos' minions, like the monsters he commands, could be antagonists. For instance, the dracaenae. They are always eager to prove themselves to Kronos and might see Percy as competition within Kronos' ranks. They could constantly try to undermine Percy's position and cause trouble for him.
The other Titans could be main antagonists. For example, Hyperion who is known for his great strength and his desire for destruction. He might not fully trust Percy and constantly try to undermine him in Kronos' eyes. Another could be Atlas, who is already a major foe in the Percy Jackson series. He might see Percy as a threat to his own plans within Kronos' regime.
Maybe there are some original characters created by the fanfiction author. These characters could have their own unique abilities and backstories. They might be the ones who tip the scales in Percy's favor, for instance, by having a special power that weakens Kronos just before Percy makes the final blow.
Well, the main antagonists could be a group of rogue demigods who have formed a cult around Kronos. They believe that Percy, as the heir of Kronos, should lead them in overthrowing the current order of the demigod world. But Percy doesn't want any part of it, so they become his enemies. Another possible antagonist could be an ancient being that was once in league with Kronos and now sees Percy as a means to resurrect Kronos or continue his dark legacy. This being would stop at nothing to force Percy to embrace his role as the heir.
Perhaps there are some traitors from the other side. These characters, seeing Kronos' power and potential for victory, switch sides and help him in the war. They might provide valuable information about the enemy's defenses and plans.
In this fanfiction, it could be some of the Titans who are still loyal to Kronos' old ways. They might see Percy as a tool to bring back Kronos' full power. They would try to manipulate Percy into joining their cause, and when he refuses, they become the main antagonists trying to either kill him or use his power against his will. Another possible antagonist could be a powerful demigod who is jealous of Percy's new - found status and wants to take it for himself.
The Olympian gods could be the main antagonists. Since Percy is the adopted son of Kronos, they might see him as a potential threat and try to stop him before he can fulfill any of Kronos' possible plans. They may send their demigod heroes after him.
Annabeth is often a popular character. In fanfiction, she might play a crucial role in helping Percy deal with his complex identity as the son of Kronos. Grover could also be popular as he's Percy's loyal friend and could be there to support Percy through his struggles related to his new - found heritage.
One possible plot could be Percy starting off reluctantly working for Kronos. Maybe Kronos has some sort of leverage over Percy, like threatening his friends or family. Percy then has to play a double - agent role, secretly trying to undermine Kronos' plans while appearing to be loyal. He could gather information about Kronos' forces and weaknesses and pass it on to the good guys.
Luke could also be a prominent character. Since he has a complex relationship with Kronos in the original story, in fanfiction he could play a role in either helping or hindering fem Percy's efforts against Kronos. Nico di Angelo is another possibility. His powers over the dead could be useful in a fight against Kronos, and he might team up with fem Percy for that reason.
It could be the Titans who see Percy as a threat. Since he is the son of Kronos, they might want to either use him for their own purposes or eliminate him to prevent any interference in their plans.